Topics

• Reproducibility
• RStudio
• Markdown/Rmarkdown
• Reports and presentations in R

What's all the fuss about?

https://www.nature.com/collections/prbfkwmwvz/

https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970

"The difference between a scientist and a crazy person is that a scientist takes notes."

Automate workflow

• Install packages from repositories

install.packages(), devtools::install_github()

• Read data and scripts

read.delim(), source(), readr::read_tsv()

• Reorganise data

dplyr, tidyr

• Create figures

ggplot2

• Run statistics

lm(), wilcox.test()

• Run external programs

system("./plink --file --flag1 --flag2 --out bla")

R

• Multiple R versions can be installed
• Be explicit about R version
• Set up R with write permission in libraries
• Windows users install to C:/R/ rather than C:/R/Program Files/
• Windows users install rtools for compiling from source
• Linux users will need additional linux packages
• Bioconductor packages are better managed with BiocManager to avoid conflicts

RStudio • IDE

• Code completion & Syntax highlighting (for many languages)
• R Notebook
• Debugging
• Useful GUI elements
• Multiple sessions can be opened in parallel

RStudio • Project

Create a new project

• Portable project (.Rproj)
• Dynamic reports
• Version control (git)
• Package control (packrat)

Project Structure

project_name/
+-- raw/
|   +-- gene_counts.txt
|   +-- metadata.txt
+-- results/
|   +-- gene_filtered_counts.txt
|   +-- gene_vst_counts.txt
+-- images/
|   +-- exp-setup.jpg
+-- scripts/
|   +-- bash/
|   |   +-- fastqc.sh
|   |   +-- trim_adapters.sh
|   |   +-- mapping.sh
|   +-- r/
|       +-- qc.R
|       +-- functions.R
|       +-- dge.R
+-- report/
    +-- report.Rmd

• Organise data, scripts and results sensibly
• Keep projects self contained
• Use relative links

Document converter

• Rmd > md > docx|HTML|PDF
• PDF needs Latex
• Handouts
• Scientific Articles
• Presentations
  • beamer
  • ioslides
  • slidy
  • xaringan

Document formats

• Summary
• Reports in HTML, PDF, MS Word etc
• Simple web pages and websites using Rmarkdown
• Complex websites using blogdown
• Books using bookdown
• Package documentation using pkgdown
• Web applications and interactive documents using Shiny
• Dashboards using flexdashboard or shinydashboard

RMarkdown • Intro

Markdown

• Plain text format for readability
• Support pure HTML for complex formatting
• Many variations
  • John Gruber's original
  • GitHub Flavored Markdown (GFM)
  • Pandoc
  • MultiMarkdown
  • 
• Pandoc supports conversion to multiple output formats
• To compare MD variants

RMarkdown

• Markdown + embedded R chunks
• Combine text and code in one file
• RMarkdown mostly uses Pandoc markdown

RStudio • Notebook

Create a new .Rmd document

• Text and code can be written together
• Inline R output (text and figures)

RMarkdown • Guide

• Create a file that ends in .Rmd
• Add YAML matter to top

---
title: "This is a title"
output: 
  rmarkdown::html_document
---

• In RStudio File > New File > R Markdown opens up an Rmd template
• Render interactively using the Knit button
• Render using command rmarkdown::render("report.Rmd")

RMarkdown • Guide

### Heading 3
#### Heading 4
_italic text_  
__bold text__  
`code text`  
~~strikethrough~~  
2^10^  
2~10~  
- bullet point
Link to [this](somewhere.com)
![](https://www.r-project.org/Rlogo.png)

RMarkdown • Guide

• R code can be executed inline like this

Today's date is `r date()`
Today's date is Fri Jun 7 12:43:36 2019

• R code can be executed in code chunks

```{r}
date()
```

• By default shows input code and output result.

date()

## [1] "Fri Jun  7 12:43:36 2019"

• Many arguments to tweak chunks
  • Set eval=FALSE to not evaluate a code chunk
  • Set echo=FALSE to hide input code
  • Set results="hide" to hide output

R Markdown reference https://rmarkdown.rstudio.com/